In urban Australia, untreated sewage enters local waterways when sewerage systems are overloaded or breakdown. Our aim was to assess the impacts of sewage overflows and potential risks to public and ecosystem health in the tidal waterways of the coastal suburb of Lota, Brisbane using microbiological and chemical indicators. Expectations for improved sewerage system performance are driven by the belief that sewage overflows cause significant environmental harm. However the research here shows in a large wet weather event, stormwater and not the overflow was the dominant stressor of ecological health. Even in the dry weather overflow event impacts were likely low and restricted to the mixing zone at the point of overflow. However, sewage overflows, in dry and wet weather, did pose an unacceptably high public health hazard to potential swimmers in Lota Creek until the overflow stopped and there was a complete tidal exchange with the estuary. This Brisbane City Council/Brisbane Water and Costal CRC funded project has provided a sound scientific basis for quantifying overflow impacts and prioritising management of overflows and stormwater in a wetland estuary. It has also identified the need to develop programs to educate and raise community awareness, assess waterway use and potential pathways that can pose a risk to human health from wet and dry weather overflows both locally and into Moreton Bay.